Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_015738681.1 ADEG_RS03355 shikimate dehydrogenase
Query= SwissProt::Q58484 (282 letters) >NCBI__GCF_000024605.1:WP_015738681.1 Length = 297 Score = 219 bits (559), Expect = 4e-62 Identities = 122/282 (43%), Positives = 169/282 (59%), Gaps = 8/282 (2%) Query: 2 INAKTKVIGLIGHPVEHSFSPIMHNAAFKDKGLNYVYVAFDVLPENLKYVIDGAKALGIV 61 I+ T+++G+ G P+ H+ SP MHNAAF+ LNY+YV F V E L +AL + Sbjct: 3 IDGNTRIVGIFGDPIAHTLSPHMHNAAFRALNLNYIYVPFWVRREELAEATAAIRALNLA 62 Query: 62 GFNVTIPHKIEIMKYLDEIDKDAQLIGAVNTIKIEDGKAIGYNTDGIGARMALEEEIGRV 121 G NVT+PHK I+ YLDE++++A LIGAVNT+ + GK G NTD G AL+EE Sbjct: 63 GVNVTVPHKEAIIPYLDELEEEACLIGAVNTVVNQGGKLWGSNTDASGFLAALQEEGFAP 122 Query: 122 KDKNIVIYGAGGAARAVAFELAKD--NNIIIANRTVEKAEALAKEIAEKLNKK-----FG 174 K + + GAGGAARAV LA+ I NRT ++A LA + E+ + + Sbjct: 123 AKKKVAVLGAGGAARAVGVALARSQVEEITFFNRTFDRAAELAAYLEERTGVRARALPWE 182 Query: 175 EEVKFSGLDVDLDGVDIIINATPIGMYPNIDVEPIVKAEKLREDMVVMDLIYNPLETVLL 234 E F G++ L D+I+ T +GM+P P V E R +V+DL+Y PL+T L Sbjct: 183 EMGSFRGIEF-LQAADLIVQTTSLGMHPREGEMPPVAEEAFRPGQLVIDLVYRPLKTRFL 241 Query: 235 KEAKKVNAKTINGLGMLIYQGAVAFKIWTGVEPNIEVMKNAI 276 A+K AKT +GLGML+YQGA+AF +WTGV +EVM+ A+ Sbjct: 242 SLAQKRGAKTASGLGMLLYQGALAFSLWTGVPAPLEVMRAAL 283 Lambda K H 0.318 0.139 0.385 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 206 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 282 Length of database: 297 Length adjustment: 26 Effective length of query: 256 Effective length of database: 271 Effective search space: 69376 Effective search space used: 69376 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_015738681.1 ADEG_RS03355 (shikimate dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00507.hmm # target sequence database: /tmp/gapView.12154.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00507 [M=270] Accession: TIGR00507 Description: aroE: shikimate dehydrogenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-84 267.2 0.0 7.5e-84 267.0 0.0 1.0 1 lcl|NCBI__GCF_000024605.1:WP_015738681.1 ADEG_RS03355 shikimate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_015738681.1 ADEG_RS03355 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 267.0 0.0 7.5e-84 7.5e-84 2 269 .. 9 287 .. 8 288 .. 0.92 Alignments for each domain: == domain 1 score: 267.0 bits; conditional E-value: 7.5e-84 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++g++G+pi+h +sp +hnaa++ l+l++ Y+ f v+ eel +a +i+al l GvnvTvP+Ke+++++ lcl|NCBI__GCF_000024605.1:WP_015738681.1 9 IVGIFGDPIAHTLSPHMHNAAFRALNLNYIYVPFWVRREELAEATAAIRALNLAGVNVTVPHKEAIIPY 77 78******************************************************************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 lDe+ee+a ligavNT++ ++gkl g nTD+ G++++L++ + ++k+v+++GAGGaa+av ++L++ lcl|NCBI__GCF_000024605.1:WP_015738681.1 78 LDELEEEACLIGAVNTVVNQGGKLWGSNTDASGFLAALQEEGFAPAKKKVAVLGAGGAARAVGVALARS 146 ****************************************8888889********************98 PP TIGR00507 140 .dkeviiaNRtvekaeelaerlqe..........lgeilalsleeve.lkkvdliinatsaglsgeid. 195 +e++ +NRt+++a ela l+e e+ ++ +e l+ dli+++ts+g+++ lcl|NCBI__GCF_000024605.1:WP_015738681.1 147 qVEEITFFNRTFDRAAELAAYLEErtgvraralpWEEMGSFR--GIEfLQAADLIVQTTSLGMHPREGe 213 4578*****************999866655443333333333..34414559*************9985 PP TIGR00507 196 eaevkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264 ++v +e ++ g+lv+Dlvy pl+t +l++a+k+g+k++ GlgMl +Q+al+F lwtgv ++e+++ a lcl|NCBI__GCF_000024605.1:WP_015738681.1 214 MPPVAEEAFRPGQLVIDLVYRPLKTRFLSLAQKRGAKTASGLGMLLYQGALAFSLWTGVPAPLEVMRAA 282 689****************************************************************** PP TIGR00507 265 lkekl 269 l+e+l lcl|NCBI__GCF_000024605.1:WP_015738681.1 283 LEEAL 287 99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (297 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.60 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory